Phylogenetic Analysis of Antarctic Notothenioids Illuminates the Utility of 7 Radseq for Resolving Cenozoic Adaptive Radiations
Total Page：16
File Type：pdf, Size：1020Kb
0ROHFXODU3K\ORJHQHWLFVDQG(YROXWLRQ ² Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogenetic analysis of Antarctic notothenioids illuminates the utility of 7 RADseq for resolving Cenozoic adaptive radiations Thomas J. Neara,b,⁎, Daniel J. MacGuigana, Elyse Parkera, Carl D. Struthersc, Christopher D. Jonesd, Alex Dornburge a Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA b Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA c Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand d Antarctic Ecosystem Research Division, NOAA Southwest Fisheries Science Center, La Jolla, CA 92037, USA e North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA ARTICLE INFO ABSTRACT Keywords: Notothenioids are a clade of ∼120 species of marine fishes distributed in extreme southern hemisphere tem- Notothenioidei perate near-shore habitats and in the Southern Ocean surrounding Antarctica. Over the past 25 years, molecular Phylogenomics and morphological approaches have redefined hypotheses of relationships among notothenioid lineages as well Phylogenetic informativeness as their relationships among major lineages of percomorph teleosts. These phylogenies provide a basis for in- Signal noise vestigation of mechanisms of evolutionary diversification within the clade and have enhanced our understanding Icefishes of the notothenioid adaptive radiation. Despite extensive efforts, there remain several questions concerning the phylogeny of notothenioids. In this study, we deploy DNA sequences of ∼100,000 loci obtained using RADseq to investigate the phylogenetic relationships of notothenioids and to assess the utility of RADseq loci for lineages that exhibit divergence times ranging from the Paleogene to the Quaternary. The notothenioid phylogenies inferred from the RADseq loci provide unparalleled resolution and node support for several long-standing problems including, (1) relationships among species of Trematomus, (2) resolution of Indonotothenia cyano- brancha as the sister lineage of Trematomus, (3) the deep paraphyly of Nototheniidae, (4) the paraphyly of Lepidonotothen s.l., (5) paraphyly of Artedidraco, and 6) the monophyly of the Bathydraconidae. Assessment of site rates demonstrates that RADseq loci are similar to mtDNA protein coding genes and exhibit peak phylo- genetic informativeness at the time interval during which the major Antarctic notothenioid lineages originated and diversified. In addition to providing a well-resolved phylogenetic hypothesis for notothenioids, our analyses quantify the predicted utility of RADseq loci for Cenozoic phylogenetic inferences. 1. Introduction economic importance for international fisheries interests (Constable et al., 2000; Abrams, 2013). Despite a long history of research, a well- Antarctic notothenioids (Cryonotothenioidea) are one of the most resolved species-level phylogeny of notothenioids is not available and well studied groups of marine fishes and one of few examples of marine several key phylogenetic questions remain unanswered. teleost adaptive radiation (Eastman, 1993; Clarke and Johnston, 1996; Over the past quarter-century efforts to investigate the phyloge- Ingram and Mahler, 2011; Matschiner et al., 2011; Near et al., 2012; netics of notothenioids have resulted in important discoveries that Colombo et al., 2015; Dornburg et al., 2017a). In addition to exhibiting dramatically altered subsequent taxonomic classifications. For example, an interesting evolutionary history, notothenioids are vital to Antarctic early morphological and molecular inferred phylogenies resolve marine ecosystems, as they comprise a substantial component of the Bovichtidae, historically delimited to include Bovichtus, Cottoperca, and biomass, abundance, and species diversity of near shore fishes Pseudaphritis(Eastman, 1993; Nelson, 1994), as paraphyletic and Ele- (Eastman, 1993, 2005). Correspondingly, these species are critical in ginops maclovinus as the sister lineage of Cryonotothenioidea instead of linking lower level consumers and higher level predators in the Ant- being closely related to the nototheniid lineage Dissostichus (Balushkin, arctic marine food web (La Mesa et al., 2004), including species of high 1992; Lecointre et al., 1997; Bargelloni and Lecointre, 1998). The most ⁎ Corresponding author at: Department of Ecology & Evolutionary Biology, Yale University, P.O. Box 208106, New Haven, CT 06520, USA. E-mail address: [email protected] (T.J. Near). https://doi.org/10.1016/j.ympev.2018.09.001 Received 10 April 2018; Received in revised form 31 August 2018; Accepted 1 September 2018 $YDLODEOHRQOLQH6HSWHPEHU (OVHYLHU,QF$OOULJKWVUHVHUYHG T.J. Near et al. 0ROHFXODU3K\ORJHQHWLFVDQG(YROXWLRQ ² recent phylogenetic analyses of notothenioids use DNA sequences 2007; Townsend et al., 2012). Our results provide a strongly supported sampled from multiple mitochondrial and nuclear genes with a taxon phylogenetic hypothesis of notothenioid species-level relationships, the sampling that includes most of the recognized species in the clade (Near ability to reject several previous phylogenetic hypotheses and refine our et al., 2012; Dornburg et al., 2017a). While these studies provide im- perspective on the predicted utility and limits of RADseq data. portant insights into the relationships of notothenioids and serve as the basis for comparative analyses investigating the history and mechan- 2. Methods isms of notothenioid diversification (Near et al., 2012; Dornburg et al., 2017a), there are several unresolved issues in the phylogenetics of 2.1. Taxon sampling, sequencing, and data preparation notothenioids: the lack of phylogenetic resolution among the ∼14 species of the rapidly diversifying Trematomus (Kuhn and Near, 2009; The taxon sampling included 80 notothenioid species Janko et al., 2011; Lautredou et al., 2012; Near et al., 2012); the re- (Supplementary Table 1), which encompasses all of the recognized solution of the neutrally buoyant Pleuragramma antarctica among the taxonomic families and is very similar to previous phylogenetic studies major lineages of Cryonotothenioidea (Near and Cheng, 2008; Dettaï using Sanger sequenced legacy markers (Near et al., 2012). For ex- et al., 2012; Near et al., 2012); and the lack of support for monophyly of ample, the species included in Near et al. (2012) that are not included the Antarctic Dragonfishes (Bathydraconidae) in molecular analyses in this study are Gobionotothen acuta, G. marionensis, Paranotothenia (Bargelloni et al., 2000; Derome et al., 2002; Dettaï et al., 2012; Near angustata, Bathydraco scotiae, Neopagetopsis ionah, and Cryodraco ant- et al., 2012). These remaining challenges to the resolution of notothe- arcticus. Species included in this study that are not in Near et al. (2012) nioid phylogeny inhibit the investigation of important questions, such are Nototheniops cf. nudifrons, Pogonophryne fusca, and Bathydraco as the origin of neutral buoyancy (Near et al., 2007, 2012), species joannae. We are confident that the minor differences in taxon sampling relationships within rapidly diversifying lineages (e.g., Trematomus & do not have a strong effect on the phylogenetic inferences. Artedidraconidae; Lecointre et al., 2011; Lautredou et al., 2012), and DNA was isolated from tissue samples using the Qiagen DNeasy patterns of hemoglobin evolution in Bathydraconidae that led to the tissue extraction protocols (DNeasy, Qiagen, Valencia, CA). Extractions loss of this protein in the Crocodile Icefishes (Channichthyidae) were gel-quantified in agarose using New England Biolabs 100 bp (Bargelloni et al., 1998; Near et al., 2006; Lau et al., 2012). ladder (NEB, Ipswich, MA) to ensure successful extractions and DNA Next-generation sequencing through reduced representation concentrations were determined using a Qubit v. 3.0 fluorometer methods such as restriction site associated DNA sequencing (RADseq) (ThermoFisher Scientific, Philadelphia, PA). All DNA extractions were hold the promise of resolving species-level relationships in notothe- standardized to contain between 17 and 23 ng DNA/µL. nioids. By sequencing DNA flanking restriction sites, RADseq captures The RADseq protocol was not optimized for notothenioids, but ra- thousands of single nucleotide polymorphisms (SNPs) across any target ther is a single enzyme protocol that has been used in lineages of genome and have been used to resolve difficult phylogenetic problems flowering plants (Eaton et al., 2017). Floragenex Inc. (Portland, OR) in lineages spanning beetles (Cruaud et al., 2014), plants (Massatti prepared the RADseq libraries using the SbfI restriction enzyme, a six et al., 2016; Wang et al., 2017), corals (Herrera and Shank, 2016), and base pair cutter (5′-CCTGCA-3′) and sample-specific barcodes. The Lake Victoria cichlids (Wagner et al., 2013). Empirical assessments of samples were combined into two 95-sample multiplexed libraries. RADseq data suggest cost-effective phylogenetic utility across temporal Floragenex created two replicates of each library in order to minimize scales spanning recent divergences to those dating back tens of millions the influence of PCR duplication bias and other technical errors. We of years (Eaton et al., 2017). However, these assessments are based on sequenced each library twice on an Illumina HiSeq 2000 using single- post-hoc measure of topological support such as bootstrap values that end 100 base pair